[gmx-users] 3Dplot

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 4 10:13:54 CET 2009

Alessandro Casoni wrote:
> Dear gmx-users,
> i would like to generate a 3D plot of my potential energy/RMSD/radius of 
> gyration.
> I used g_energy, g_rms and g_gyrate to collect informations on my 
> simulation..any suggestion on software able to generate 3D plot?
Please check
  Marvin Seibert, Alexandra Patriksson, Berk Hess and David van der 
Spoel: Reproducible polypeptide folding and structure prediction using 
molecular dynamics simulations J. Mol. Biol. 354 pp. 173-183 (2005)

We used g_sham to combine the data and Visit (visit.llnl.gov) for the 3D 
plots. The software has evolved since then obviously, so you can 
probably make it (even) prettier now. An alternative is gnuplot.

> thanks
> alessandro
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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